Chemical tag marks future microRNAs for processing, study shows

A DNA helix is formed when two DNA strands naturally arrange themselves into a helix. However, RNA doesn't form a helix; they form hairpin-like loops instead. Typically, DNA has a single job to handle, but RNA has multiple jobs to do which includes acting as a precursor for small molecules that block the activity of genes. In order to do this the RNA molecules must be trimmed from long hairpin-loop structures. The question that raises now is  how do the cells know which RNA loops need processing and which do not?

A new research conducted at the Rockefeller University and the findings of which were published in March 18th publication of the Nature, shows how cells sort out the loops meant to encode small RNAs, known as microRNAs, by tagging them with a chemical group. Since, microRNAs help control various processes throughout the body, this discovery is quite important. It will have implications for development, health and disease, including cancer, the entry point for this research.

Sohail Tavazoie, Leon Hess Associate Professor, Senior Attending Physician and head of the Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology and the study's lead author said that the work in their lab and in many other researches earlier has shown that a number of changes happen in microRNAs in various types of cancer. In order to understand how and why this happens, a basic question need to be addressed – how cells normally identify and process microRNAs. Claudio AlarcÃ³n, a research associate in Sohail's lab discovered that cells can increase or decrease microRNAs by using a specific chemical tag.

RNAs have been long known to be something that lies between DNA and proteins. But, it turns out that they are quite versatile. A number of microRNAs have been discovered by scientists that regulate gene expression. MicroRNAs are encoded into the genome as DNA; they are later transcribed into hairpin loop RNA molecules, also known as primary microRNAs. These loops are then clipped to generate microRNA precursors.

In order to find out how cells know which hairpin loop to begin trimming, Alarcon started by looking out for modifications cells might make to the RNA molecules that are likely to transform into microRNAs.

Bioinformatics software was used to scan and find out any unusual patterns in the unprocessed RNA sequences. The sequence GGAC, code for the bases guanine-guanine-adenine-cytosine, stood out because it appeared in good number in the unprocessed primary microRNAs. The GGAC was of key importance as it led the researchers to an enzyme known as METTL3, which tags the GGAC segments with a chemical marker, a methyl group, at a particular spot on the adenine.

Once METTL3 was found, everything fell in place. Alarcon said that the methyl in adenosines (m6A tag) is the most common known RNA modification. METTL3 is known to contribute to stabilizing and processing messenger RNA, which is transcribed from DNA. Now it is known that it has a role to play in the processing of primary microRNAs.

The researchers carried out a number of experiments through which they confirmed the importance of methyl tagging, finding high levels of it near all types of unprocessed microRNAs,. It suggests that it is indeed a generic mark associated with these molecules. When the researchers reduced expression of METTL3, it was seen that unprocessed primary microRNAs got accumulated meaning that the enzyme’s tagging action was important to the process. It was also found that in cell culture and in biochemical systems, primary microRNAs processed efficiently in the presence of the methyl tags.

Tavazoie added that cells can remove these tags, as well as add them. With the help of these experiments a switch has been identified that can be used to ramp up or tamp down microRNA levels, and alter gene expression. It could prove crucial in governing cancer progression.